Flashtool is a flashing software that can be used to :
Flash original Images (Android 1.6, 2.1, 2.3 Images)
Root your phone
Install Recovery, Busybox, custom kernels
Clean your Rom (remove /system/apps apps of your choice) (Be careful, unless you really know what you do, do not modify the default list. This can make your phone stuck at the SE Logo)
Clear dalvik cache
Optimize (install of JIT v2) (Disabled in 0.4, will readd it as a plugin for 2.1 phones only)
Customize (installs apps found in the custom/apps folder of the flashtool)
Clean uninstalled (remove any references to system apps removed in the Clean (root needed) step)
Edit any text file on the device
Rebrand your device